thesis, and each product serves as the exclusive sub- strate for the next enzyme in the series. See A, B antigens, glycosylation. oligospermia an abnormally low concentration of sperm in the semen. OMIA On-line Mendelian Inheritance in Animals, a catalogue of animal species, especially domesti- cated ones where the molecular basis of genetic dis- eases has been studied (cat, cattle, chicken, dog, donkey, fox, goat, guinea pig, hamster, horse, llama, mink, mouse, pig, pigeon, rabbit, rat, Rhesus mon- key, sheep, turkey, and zebra fish). The database lists such diseases as lysosomal storage diseases, in- herited bleeding diseases, dwarfism, retinal defects, sex reversals, and muscular dystrophies. See Appen- dix E, Individual Databases. OMIM On-line Mendelian Inheritance in Man, an electronic catalog of inherited human diseases. The catalog has been available on-line since 1987. It is updated weekly and accessible through the Internet. See Appendix E, Individual Databases; human genetic diseases. ommatidium one of the facets making up the compound eye of insects.
The frontispiece illustra- tion shows the right compound eye of a fruit fly. It is composed of a honey comb-like array of facets. An eye contains about 750 ommatidia, and each is made up of 8 photoreceptor cells and 11 accessory cells arranged in a precise three-dimensional pattern. There are 6 outer and 2 inner photoreceptor cells (the outer ones are labeled R1-R6 and the inner ones R7 and R8). Each photoreceptor cell contains a rhabdomere (q.v.) in which rhodopsin (q.v.) is stored.
The rhabdomere functions like the discs in the outer segments of the photoreceptor cells of the vertebrate retina (see the illustration on page 385). Overlying the photocells is a quartet of cone cells. Primary pigment cells surround the cone cells, and secondary pigment cells lie between adjacent omma- tidia. The ommochrome and drosopterin pigments are stored in the pigment cells. See Drosophila eye pigments, eyeless, sevenless. ommochromes See Drososphila eye pigments. omnipotent suppressors nonsense suppressors in yeast that are codon nonspecific, act only upon UAA and UAG mutations, and fall into two complemen- tation groups. They are thought to be mutations of ribosomal components rather than suppressor muta- tions in tRNAs since these are codon specific. oncogene a gene that induces uncontrolled cell proliferation. Some oncogenes were originally of cel- lular origin but now reside in the genomes of retrovi- ruses (q.v.). Here they have acquired the ability to transform cells to a neoplastic state. The v-src gene of the Rous sarcoma virus (q.v.) and the v-sis gene of the simian sarcoma virus (q.v.) are examples.
On- cogenes also have been isolated from tumors that have arisen spontaneously or have been induced by chemical carcinogens. Finally, there are oncogenes that reside in oncogenic viruses with DNA genomes. The polyoma virus (q.v.) and simian virus 40 (q.v.) are examples. Viral and cellular oncogenes arise from cellular proto-oncogenes (q.v.), which play a role in the control of normal cell proliferation. See Appendix C, 1981, Parker et al.; 1982, Reddy et al.; Appendix E; myc, oncogenic virus, oncomouse, Ti plasmid, T24 oncogene. oncogene hypothesis a proposal that carcinogens of many sorts act by inducing the expression of ret- rovirus genes already resident in the target cell.
It is now known that while cells from different species harbor genes homologous to retrovirus oncogenes, the cellular genes were the progenitors of the viral oncogenes. The cellular genes are now called proto- oncogenes (q.v.) and they evidently function in the normal physiology of cells from evolutionarily di- verse species. See Appendix C, 1969, Huebner and Todaro. oncogenic virus a virus that can transform the cells it infects so that they proliferate in an uncon- trolled fashion. See Appendix C, 1910, Rous; 1981, Parker et al.; 1983, Doolittle et al.; Abelson mouse leukemia virus, Friend leukemia virus, Gross mouse leukemia virus, Harvey rat sarcoma virus, human papil- lomavirus, Moloney leukemia virus, mouse mammary tumor virus, polyoma virus, Rauscher leukemia virus, retroviruses, Rous sarcoma virus, Shope papilloma vi- rus, simian sarcoma virus, simian virus 40, transforma- tion. oncolytic capable of destroying cancer cells. oncomouse a laboratory mouse carrying activated human cancer genes. Du Pont started selling onco- mice late in 1988. They were the first transgenic ani- mals to be patented. These mice carry the ras onco- gene plus a mouse mammary tumor virus promoter. This ensures that the oncogene is activated in breast tissue, and the mice develop breast cancer a few months after birth. See Appendix C, 1988, Leder and Stewart. oncornavirus an acronym for oncogenic RNA virus. See retrovirus.
One gene-one enzyme hypothesis
one gene-one enzyme hypothesis the hypothesis that a large class of genes exists in which each gene controls the synthesis or activity of but a single en- zyme. See Appendix C, 1941, Beadle and Tatum; 1948, Mitchell and Lein. one gene-one polypeptide hypothesis the hy- pothesis that a large class of genes exists in which each gene controls the synthesis of a single polypep- tide. The polypeptide may function independently or as a subunit of a more complex protein. This hy- pothesis replaced the earlier one gene-one enzyme hypothesis once heteropolymeric enzymes were dis- covered. For example, hexosaminidase (q.v.) is en- coded by two genes. See two genes-one polypeptide chain. one-step growth experiment the classic proce- dure that laid the foundation for the quantitative study of the life cycle of lytic bacterial viruses. A suspension of bacteria was mixed with enough vi- ruses to ensure that a virus attached to each host cell. Free viruses were removed, and at periodic in- tervals thereafter aliquots were withdrawn and sub- jected to plaque assay (q.v.). The number of plaques per aliquot remained constant for an initial period of time. Aliquots taken after this latent period showed a progressive increase in plaque numbers.
During this time, infected cells were lysing and liberating in- fectious phage, each capable of producing a plaque. Once all cells had lysed, a plateau was reached, and so the curve describing plaque counts during the ex- periment showed a single step. The eclipse period re- fers to the time between viral attachment and the assembly of the first progeny phage. It is during this period that replication and assembly of the phages is occurring. Cells must be artificially lysed to deter- mine when the earliest infectious particles appear. The latent period is longer than the eclipse period because the host cell does not normally lyse until many progeny have been assembled. See Appendix C, 1939, Ellis and Delbru¨ck; burst size, plaque. ONPG o-nitrophenyl galactoside, an unnatural substrate for beta galactosidase. It is cleaved by this enzyme (see illustration) into galactose and o-nitro- phenol (a yellow compound, easily assayed spectro- photometrically). ONPG has been extensively used to determine enzyme activity associated with mu- tants of the lac operon (q.v.) in E. coli. Unlike IPTG (q.v.), ONPG is not an inducer of the operon, so these two substances are often used in combination. ontogeny the development of the individual from fertilization to maturity.
Onychophora a phylum of about 70 species that are all topical or subtropical in distribution. They are commonly called peripatus or velvet worms. They are terrestrial and have between 14 and 43 pairs of unsegmented walking legs. Earlier forms were ma- rine, and their fossils are found in rocks dating back to the Cambrian. Peripatus is sometimes called a liv- ing fossil (q.v.), and it shows a mixture of annelid and arthropod characters. Since it molts, it is placed in the Ecdysozoa (q.v.). oocyte the cell that upon undergoing meiosis forms the ovum. oogenesis the developmental process that results in the formation of the egg. Oogenesis involves a se- quence of events, including mitotic proliferation of oogonial cells, meiotic divisions in the oocyte, vitel- logenesis (q.v.) and oocyte growth, synthesis and lo- calization of maternal products in the oocyte, speci- fication of egg polarity, and formation of egg membranes. Most of these events entail interactions between the germ line (q.v.) and the surrounding soma (q.v.). See insect ovary types. oogonium 1. the female gametangium of algae and fungi. Contrast with antheridium. 2. in animals, a mitotically active germ cell that serves as a source of oocytes. The stem cell shown on page 98 is an oogonium. ookinete See Plasmodium life cycle. oolemma the plasma membrane of the ovum. ooplasm the cytoplasm of an oocyte.
ootid nucleus one of the four haploid nuclei formed by the meiotic divisions of a primary oocyte. Three of the nuclei are discarded as polar nuclei and the remaining one functions as the female pronu- cleus. See oriented meiotic division, polar body. opal codon the mRNA stop codon UGA. See amber codon, ochre codon. opaque-2 a mutant strain of corn that produces an increase in the lysine content of seeds. This was the first mutation shown to improve the amino acid bal- ance in the proteins of an agriculturally important plant. Animal proteins, such as those in milk and beef, have a better balance of certain essential amino acids (like tryptophan and lysine) than do plant pro- teins. Mutants like opaque 2 are of potential use in combating kwashiorkor (q.v.). See Appendix C, 1964, Mertz et al., zein.
open population a population that is freely ex- posed to gene flow (q.v.). open reading frame See reading frame. operational definition a definition in terms of properties significant to a given experimental situa- tion, without consideration of the more fundamental characteristics of the defined subject. operator a chromosomal region capable of inter- acting with specific repressors, thereby controlling the function of adjacent cistrons. See lac operon, reg- ulator gene. operon a unit that consists of one or more cistrons that function coordinately under the control of an operator.
The genome of the E. coli strain sequenced in 1997 contained about 2,200 operons. Of these, 73% had only one gene, 17% had two, 5% had three, and the rest had four or more. See Appendix C, 1961, Jacob and Monod; 1997, Blattner et al.; regulator gene. operon network a collection of operons and their associated regulator genes that interact in the sense that the products of structural genes in one operon serve to suppress or activate another operon by act- ing as repressors or effectors. opine a compound, specifically synthesized by crown gall plant cells, that can be used by agrobac- teria as specific growth substances. Examples are no- paline [N-α-(1,3-dicarboxylpropyl)-L-arginine] and octopine [N-α-(D-1-carboxyethyl)-L-arginine].
See Agrobacterium tumefaciens. opisthe the posterior daughter organism produced in a transverse division of a protozoan. opisthokonta a monophyletic supergroup that contains animals and fungi. The conclusion that the Fungi are a sister group to Animalia and that fungi and plants belong to independent lineages is based on sequence data from SSU rRNAs and certain ubiq- uitous proteins. See Appendix A, Kingdoms 3 and 4; Appendix C, 1993, Baldauf and Palmer; 16S rRNA, translation elongation factors. opportunism a theory that (1) all potential modes of existence will eventually be tried by some group and all potential niches will eventually become oc- cupied, and (2) organisms evolve only as historical conditions permit and not according to what would theoretically be best.
opportunistic species a species specialized to ex- ploit newly opened habitats because of its ability to disperse for long distances and to reproduce rapidly. opsin the protein portion of a photosensitive mol- ecule contained in the discs of the photoreceptors of the retina (q.v.). An opsin (see page 312) is a chain of amino acids, running from the amino-terminal end (N), exposed on the external aqueous surface of the disc, to a carboxyl terminal region (C), exposed to the internal aqueous surface of the disc. The chain has seven alpha helices that span the mem- brane. An opsin does not itself absorb light.
Retinal (q.v.) is the chromophore that lies within the cluster of helices and undergoes a change in shape upon re- ceiving a photon of light. See multiple transmem- brane domain proteins. opsonin any substance that promotes cellular pha- gocytosis. When antibodies bind to antigens by their Fab portions (see immunoglobulin), the shape of the molecule changes to expose the Fc region. Scavenger cells such as macrophages have Fc receptors on their surfaces. Thus, phagocytic cells can bind to and en- gulf antigen-antibody complexes. Neutrophils and macrophages have receptors for certain activated complement components. Thus, antigen-antibody- complement complexes also enhance phagocytosis through immune adherence. IgG antibodies are much more effective opsonins than IgM in the ab- sence of complement, but IgM antibodies are more effective opsonins in the presence of complement. optical antipodes enantiomers (q.v.). optical density See Beer-Lambert law.
optical isomers molecular isomers that in solution cause the rotation of the plane of a beam of plane- polanzed light passed through the solution. The ro- tation is due to the asymmetry of the molecule. Mol- ecules with this property are given the prefix D or L depending on whether the plane is rotated to the right (dextro) or to the left (levo, laevo). orange G an acidic dye often used in cytochem- istry.
ordered octad See ordered tetrad. ordered tetrad a linear sequence of four haploid meiotic cells (or pairs of each of four haploid cells produced by a postmeiotic division) within a fungal ascus. This physical arrangement allows identifica- tion of chromatids participating in crossover events. Drawing A (page 313) illustrates that, in a tetrad heterozygous for alleles controlling ascospore pig- mentation, single crossovers between these genes and the centromere will generate spores showing 2-2-2-2 and 2-4-2 segregation patterns. Drawing B illustrates that in Neurospora such patterns are ob- served, together with noncrossover asci showing 4-4 distributions. Ordovician a period in the Paleozoic era during which marine invertebrates diversified. Brachiopods were the dominant species.
The Cambrian genera of trilobites (q.v.) were replaced by new forms. The echinoderms bloomed with starfish, brittle stars, echinoids, and crinoids making their first appear- ances. Corals are found for the first time early in the Ordovician. Jawless fishes appeared and represent the first vertebrates. The Ordovician ended with a mass extinction during which the trilobites lost 50% of all families. See geologic time divisions. ORF the symbol for open reading frame See read- ing frame, URF. organ culture the maintenance or growth of organ primordia or the whole or parts of an organ in vitro in a way that may allow further differentiation or the preservation of architecture or function or both. See also in vivo culturing of imaginal discs. organelle any complex structure that forms a component of cells and performs a characteristic function. Extensively studied organelles include: centrioles, chloroplasts, the endoplasmic reticulum, Golgi material, kinetosomes, lysosomes, micro- bodies, mitochondria, peroxisomes, proteosomes, quantasomes, ribosomes, and spindles (all of which see).
organic 1. pertaining to organisms (dead or alive) or to the chemicals made by them. 2. chemical com- pounds based on carbon chains or rings. They may also contain oxygen, hydrogen, nitrogen, and various other elements. organizer a living part of an embryo that exerts a morphogenetic stimulus upon another part, bringing about its determination and morphological differen- tiation. See goosecoid, Spemann-Mangold organizer. organogenesis the formation of organs. Oriental designating one of the six biogeographic realms (q.v.) of the globe, including the southern coast of Asia east of the Persian Gulf, the peninsula of India south of the Himalayas, eastern India, south China, Sumatra, Kalimantaro (Borneo), Java, Su- lawesi (Celebes), and the Philippines. See Wallace’s line. oriented meiotic division an oocyte meiotic divi- sion, as in Drosophila where the spindles are oriented in single file with their long axes perpendicular to the egg surface.
The nucleus farthest from the sur- face functions as the oocyte pronucleus. Aberrant chromosomes that are differentially distributed to the other nuclei are eliminated. origin of replication See replication origin. Origin of Species an abbreviated name for the most famous book by Charles Darwin that docu- mented the phenomenon of evolution and elabo- rated a theory to explain its mechanism. The full ti- tle of the book was On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. The first edition was published in 1859, and no biological treatise written before or since has produced an impact upon society equal to it. The 1,250 copies of the first edition were sold out the first day. The Origin went through six editions, the last in 1872. ori site a 422 base-pair segment of the E. coli chro- mosome where replication is initiated. See replicon.
ornithine cycle a cyclic series of reactions in which potentially toxic, nitrogenous products from protein catabolism are converted to urea that is in- nocuous. In the cycle diagrammed on page 315, am- monia is removed from the system and used in the conversion of ornithine to citrulline. Aspartic acid enters the cycle, and its amino group is incorporated into arginosuccinic acid before it can form ammonia.
Arginosuccinic acid is converted to arginine, and the fumaric acid released enters the citric acid cycle (q.v.). Urea splits off arginine and regenerates orni- thine. In humans, mutants are known that block the cycle at any one of its steps, as shown in the dia- gram. Blocking produces disorders that include: or- nithine transcarbamylase deficiency, from blocking of step 1; citrullinuria (condensing enzyme defi- ciency), step 2; arginosuccinic aciduria (arginosucci- nase deficiency), step 3; lysine intolerance (inhibi- tion of arginase by excess lysine), step 4. orphan drugs pharmaceuticals developed to treat diseases that afflict relatively few people. orphans a name coined for previously undiscov- ered protein-coding ORFs, revealed by genome se- quencing, that have no clear-cut homologs in any organisms. For example, 30% of the ORFs in Sac- charomyces cerevisiae are orphans.
Orphans and URFs are synonyms. orphan viruses viruses found in the digestive and respiratory tracts of healthy people; hence they are nonpathogenic (orphan = without an associated dis- ease). See reovirus. orphons dispersed, single pseudogenes (q.v.) de- rived from tandemly repeated families or gene clus- ters, such as those for histones or hemoglohins. Or- phons may serve as a reservoir of sequences that can evolve new functions, and have probably been im- portant factors in the evolution of higher organisms. See hemoglobin genes. ortet the single ancestral organism that produced a clone of genetically identical organisms (ramets) by budding. See modular organisms, ramets. orthochromatic dye a dye that stains tissues a sin- gle color in contrast to a metachromatic dye (q.v.). orthogenesis the concept of unidirectional change during the evolution of a group of related organisms.
For example, the fossil record of the horse family (Equidae) shows a tendency toward an increase in the size of adults when more recent species are com- pared with ancestral ones. Trends of this sort were used in the past as evidence that evolution was driven toward a desired end by mystical forces. A diagram of orthogenic evolution through time shows a straight line with no side branches, since the ances- tor evolves into a new species with no temporal overlap of ancestors and descendants. More detailed studies showed subsequently that the horse evolu- tionary tree contains dozens of side branches and that many new species coexisted in time with their immediate ancestors. Contrast with cladogenesis. See Appendix C, 1951, Simpson; Hyracotherium.